sorry to hear about your child's struggle. It sounds like you are doing some good things, take heart, things can get better. If you search this forum for all messages by me, you will see that our son had just about the same situation. it was horrible. he is now 3.5 years old, and has no sign of skin issues. we still have to feed him very carefully however.
re bacterial infections, you can find many options. Manuka honey is one I know. also, if you go to http://www.earthclinic.com,
you can find many other suggestions for staph when you look at the remedies section.
with our son, classical homeopathy was a big help, as was avoiding triggers. the key seemed to be that his digestive system was underdeveloped. he had some bad nutritional deficiencies as a result. we worked with a "reams tester" (Dr. Carey Reams) to help address some of the deficencies, expensive, but useful.